Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005422.1 Hibiscus syriacus cultivar Beakdansim tig00012438_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 162166
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:951 original size:18 final size:20
Alignment explanation
Indices: 912--978 Score: 102
Period size: 18 Copynumber: 3.4 Consensus size: 20
902 GGGCTATGTA
912 CATCGATGAACATTCAATATG
1 CATCGATG-ACATTCAATATG
933 CATCGATG-CATTC-ATATG
1 CATCGATGACATTCAATATG
*
951 CATCGATGCCATTCAATATG
1 CATCGATGACATTCAATATG
971 CATCGATG
1 CATCGATG
979 CACTCTGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.30
19 10 0.23
20 13 0.30
21 8 0.18
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (20 bp):
CATCGATGACATTCAATATG
Found at i:971 original size:20 final size:20
Alignment explanation
Indices: 912--979 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
902 GGGCTATGTA
*
912 CATCGATGAACATTCAATATG
1 CATCGATG-CCATTCAATATG
933 CATCGATG-CATTC-ATATG
1 CATCGATGCCATTCAATATG
951 CATCGATGCCATTCAATATG
1 CATCGATGCCATTCAATATG
971 CATCGATGC
1 CATCGATGC
980 ACTCTGATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.29
19 10 0.22
20 14 0.31
21 8 0.18
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (20 bp):
CATCGATGCCATTCAATATG
Found at i:1061 original size:61 final size:62
Alignment explanation
Indices: 990--1108 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
980 ACTCTGATAA
* * *
990 AATAAAAACATCTAATGCCATTAGTGCATCGATGCATAAGGAGT-ATCGATGCACCCCATTG
1 AATAAAAACATCGAATGCCATTAGTGAACCGATGCATAAGGAGTCATCGATGCACCCCATTG
** * *
1051 AATAAAAACATCGAATGTGATTCGTGAACCGATGCATAAGTAGTGCATCGATGCACCC
1 AATAAAAACATCGAATGCCATTAGTGAACCGATGCATAAGGAGT-CATCGATGCACCC
1109 GTTAAGGAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 37 0.76
63 12 0.24
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (62 bp):
AATAAAAACATCGAATGCCATTAGTGAACCGATGCATAAGGAGTCATCGATGCACCCCATTG
Found at i:1713 original size:17 final size:17
Alignment explanation
Indices: 1658--1758 Score: 102
Period size: 17 Copynumber: 5.8 Consensus size: 17
1648 AGGGATATAC
1658 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCG-GACAT
1676 A--GGT--TTCGGACAAT
1 AGTGGTCCTTCGGAC-AT
1690 CAGTGGTCCTTCGGACAT
1 -AGTGGTCCTTCGGACAT
*
1708 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGG-AC-AT
1727 CAGTGGTCCTTCGGACAT
1 -AGTGGTCCTTCGGACAT
*
1745 AGTGGTTCTTCGGA
1 AGTGGTCCTTCGGA
1759 ACAATCAGTG
Statistics
Matches: 71, Mismatches: 3, Indels: 19
0.76 0.03 0.20
Matches are distributed among these distances:
13 3 0.04
14 6 0.08
15 1 0.01
16 3 0.04
17 28 0.39
18 7 0.10
19 11 0.15
20 12 0.17
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.30
Consensus pattern (17 bp):
AGTGGTCCTTCGGACAT
Found at i:1733 original size:20 final size:19
Alignment explanation
Indices: 1680--1784 Score: 119
Period size: 17 Copynumber: 5.5 Consensus size: 19
1670 AGACATAGGT
*
1680 TTCGGACAATCAGTGGTCC
1 TTCGGACAATCAGTGGTTC
1699 TTCGGAC-AT-AGTGGTTC
1 TTCGGACAATCAGTGGTTC
*
1716 TTCGGAACAATCAGTGGTCC
1 TTCGG-ACAATCAGTGGTTC
1736 TTCGGAC-AT-AGTGGTTC
1 TTCGGACAATCAGTGGTTC
1753 TTCGGAACAATCAGTGGTCTC
1 TTCGG-ACAATCAGTGGT-TC
1774 ATTCGGGACAA
1 -TTC-GGACAA
1785 ATACTGAACG
Statistics
Matches: 74, Mismatches: 3, Indels: 15
0.80 0.03 0.16
Matches are distributed among these distances:
17 24 0.32
18 8 0.11
19 13 0.18
20 18 0.24
21 2 0.03
22 7 0.09
23 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (19 bp):
TTCGGACAATCAGTGGTTC
Found at i:1734 original size:37 final size:37
Alignment explanation
Indices: 1657--1771 Score: 186
Period size: 37 Copynumber: 3.2 Consensus size: 37
1647 GAGGGATATA
1657 CAGTGGTCCTTCGAGACATA--GG-T-TTCGG-ACAAT
1 CAGTGGTCCTTCG-GACATAGTGGTTCTTCGGAACAAT
1690 CAGTGGTCCTTCGGACATAGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGGACATAGTGGTTCTTCGGAACAAT
1727 CAGTGGTCCTTCGGACATAGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGGACATAGTGGTTCTTCGGAACAAT
1764 CAGTGGTC
1 CAGTGGTC
1772 TCATTCGGGA
Statistics
Matches: 77, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
32 6 0.08
33 13 0.17
34 2 0.03
35 1 0.01
36 5 0.06
37 50 0.65
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (37 bp):
CAGTGGTCCTTCGGACATAGTGGTTCTTCGGAACAAT
Found at i:7403 original size:30 final size:30
Alignment explanation
Indices: 7367--7438 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
7357 CCCGAAGGAC
*
7367 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
7397 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
7427 CTCTCCATAGGT
1 CTATCCAGAGGT
7439 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:7541 original size:31 final size:30
Alignment explanation
Indices: 7430--7550 Score: 93
Period size: 30 Copynumber: 3.9 Consensus size: 30
7420 TCGGCAACTC
* * * * *
7430 TCCATAGGTTCCGAAGAACCTAGGTAAACTG
1 TCCATATGTTCCGTAG-ACATAAGTATACTG
* *
7461 TCCATAT-TTCCTTAGAACATAGGTATACTG
1 TCCATATGTTCCGTAG-ACATAAGTATACTG
* *
7491 TCCATATG-TCTCGAAAGACATAAGTAATTCTG
1 TCCATATGTTC-CG-TAGACATAAGT-ATACTG
*
7523 TCCATATGTTCCGTAGACATAGGTATAC
1 TCCATATGTTCCGTAGACATAAGTATAC
7551 CCTCGACTCT
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
30 31 0.42
31 23 0.32
32 17 0.23
33 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATATGTTCCGTAGACATAAGTATACTG
Found at i:8710 original size:19 final size:19
Alignment explanation
Indices: 8686--8736 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
8676 CAATAAGGGT
*
8686 ATGCATCGATGCACTACTG
1 ATGCATCGGTGCACTACTG
8705 ATGCATCGGTGCACTACTG
1 ATGCATCGGTGCACTACTG
8724 ATGCATCGGTGCA
1 ATGCATCGGTGCA
8737 TAAAATACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (19 bp):
ATGCATCGGTGCACTACTG
Found at i:10841 original size:63 final size:63
Alignment explanation
Indices: 10766--10886 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
10756 ACTCTGATAA
*
10766 AATAAAAACATCGAATGCCATTAGTGCATCGATGCATAAGGAGTGCATCGATGCACCCTAGTG
1 AATAAAAACATCGAATGCCATTAGTGCACCGATGCATAAGGAGTGCATCGATGCACCCTAGTG
** * * *
10829 AATAAAAACATCGAATGTGATTCGTGCACCGATGCATAAGTAGTGCATCGATGTACCC
1 AATAAAAACATCGAATGCCATTAGTGCACCGATGCATAAGGAGTGCATCGATGCACCC
10887 GTTAAGTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (63 bp):
AATAAAAACATCGAATGCCATTAGTGCACCGATGCATAAGGAGTGCATCGATGCACCCTAGTG
Found at i:11475 original size:18 final size:19
Alignment explanation
Indices: 11451--11506 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 19
11441 GAGGGATATA
11451 CAGTGGTCCTTCGGGACAT
1 CAGTGGTCCTTCGGGACAT
* *
11470 -AGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGGGAC-AT
11489 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
11507 AATACTGGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.45
19 3 0.10
20 14 0.45
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (19 bp):
CAGTGGTCCTTCGGGACAT
Found at i:11495 original size:20 final size:20
Alignment explanation
Indices: 11451--11507 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
11441 GAGGGATATA
11451 CAGTGGTCCTTCGGGAC-AT
1 CAGTGGTCCTTCGGGACAAT
* *
11470 -AGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGGGACAAT
11489 CAGTGGTCCTTCGGGACAA
1 CAGTGGTCCTTCGGGACAA
11508 ATACTGGACG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
20 16 0.50
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAT
Found at i:16158 original size:21 final size:21
Alignment explanation
Indices: 16133--16173 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
16123 CAGAATGGGA
*
16133 GGAATCGGTACCCCTTCATAG
1 GGAATCGATACCCCTTCATAG
16154 GGAATCGATACCCCTTCATA
1 GGAATCGATACCCCTTCATA
16174 ATATTCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
GGAATCGATACCCCTTCATAG
Found at i:16289 original size:30 final size:30
Alignment explanation
Indices: 16242--16332 Score: 157
Period size: 31 Copynumber: 3.0 Consensus size: 30
16232 AAATTTTGAA
16242 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACATTTTG
16271 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAA-CATTTTG
16302 TAAATTCAATTCAAGTCCAAAAACTATTTTG
1 TAAATTCAATTCAAGTCCAAAAAC-ATTTTG
16333 CCTTAAATTG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.19
30 12 0.20
31 36 0.61
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAAAACATTTTG
Found at i:25492 original size:6 final size:6
Alignment explanation
Indices: 25481--25510 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
25471 ATTGAGACAT
25481 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG
1 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG
25511 TTGATAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GGAAGG
Found at i:38480 original size:16 final size:15
Alignment explanation
Indices: 38456--38489 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
38446 GTAAAATCTT
*
38456 TTTTTCCCGTTCTGGA
1 TTTTCCCCG-TCTGGA
38472 TTTTCCCCGTCTGGA
1 TTTTCCCCGTCTGGA
38487 TTT
1 TTT
38490 CGATATGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (15 bp):
TTTTCCCCGTCTGGA
Found at i:38804 original size:17 final size:17
Alignment explanation
Indices: 38764--38805 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
38754 GGTTGTGATT
*
38764 GTGTTGAGTTCATTTAG
1 GTGTTGTGTTCATTTAG
38781 GTGTTGTGTTCATTTAG
1 GTGTTGTGTTCATTTAG
38798 GTGTTGTG
1 GTGTTGTG
38806 CCACCGATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.12, C:0.05, G:0.33, T:0.50
Consensus pattern (17 bp):
GTGTTGTGTTCATTTAG
Found at i:43263 original size:38 final size:36
Alignment explanation
Indices: 43150--43263 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 36
43140 TCAAATATGG
*
43150 AATTCCCATGTTCAAAGTTTGGCCAACTACCAAA-GA
1 AATTCCCATGTTCAAAGTTTGGCC-ACCACCAAATGA
* * *
43186 ATTTTCCAATGTGT-ACAAG-TTAGCCACCA--AATATGA
1 A-ATTCCCATGT-TCA-AAGTTTGGCCACCACCAA-ATGA
43222 AATTCCCATGTTCAAAGTTTGGCCACCAACCAAGATGA
1 AATTCCCATGTTCAAAGTTTGGCCACC-ACCAA-ATGA
43260 AATT
1 AATT
43264 TCCAAATTGC
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
34 6 0.10
35 18 0.30
36 8 0.13
37 14 0.23
38 14 0.23
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (36 bp):
AATTCCCATGTTCAAAGTTTGGCCACCACCAAATGA
Found at i:48017 original size:35 final size:35
Alignment explanation
Indices: 47909--48018 Score: 84
Period size: 35 Copynumber: 3.1 Consensus size: 35
47899 TTTTAGAGAT
* *
47909 CAAATATGGAATTCCCATGTTCAAAGTTTGGTCAC
1 CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
* * **
47944 CTACCAA-A-GAATTTTCCAATGTGT-ACAAG-TTAACCAC
1 C-A--AATATGAA-ATTCCCATGT-TCA-AAGTTTGGCCAC
47981 CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
1 CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
48016 CAA
1 CAA
48019 CCAAGATGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
34 6 0.11
35 20 0.36
36 7 0.13
37 16 0.29
38 6 0.11
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (35 bp):
CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
Found at i:53179 original size:42 final size:42
Alignment explanation
Indices: 53120--53200 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
53110 ACATTGTTCC
* * *
53120 GAGGTTTCGGTCGAGGCTTGAACCGGGACTTTTAGACCATCA
1 GAGGTTTCGGTCGAGGCTTAAACCAGCACTTTTAGACCATCA
*
53162 GAGGTTTCGGTCGAGGCTTAAATCAGCACTTTTAGACCA
1 GAGGTTTCGGTCGAGGCTTAAACCAGCACTTTTAGACCA
53201 ACTTTCTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (42 bp):
GAGGTTTCGGTCGAGGCTTAAACCAGCACTTTTAGACCATCA
Found at i:60167 original size:2 final size:2
Alignment explanation
Indices: 60160--60190 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60150 TCAATATACA
60160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60191 ATTTACGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60311 original size:85 final size:84
Alignment explanation
Indices: 60210--60375 Score: 210
Period size: 85 Copynumber: 2.0 Consensus size: 84
60200 ATACAATCAC
* * ***
60210 GACACACGAATGTGTGTCATCTT-TTCTAATGATGTTTGCTTCAATGACACGCAATGTA-AGTCA
1 GACACACAAATGTGTGTCATCTTATT-T-ATGACGGGGGCTTCAATGACACGCAATG-AGAGTCA
60273 TAAATGCGTGTCATAAATTTAT
63 TAAATGCGTGTCATAAATTTAT
* * *
60295 GACACACAAATGTGTGTCGTCTTCATTTATGACGGGGGCTTCAATGACGCGCAATGAGCGTCATA
1 GACACACAAATGTGTGTCATCTT-ATTTATGACGGGGGCTTCAATGACACGCAATGAGAGTCATA
60360 AATGCGTGTCATAAAT
65 AATGCGTGTCATAAAT
60376 GAGCGTCATA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 1 0.01
85 66 0.94
86 1 0.01
87 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (84 bp):
GACACACAAATGTGTGTCATCTTATTTATGACGGGGGCTTCAATGACACGCAATGAGAGTCATAA
ATGCGTGTCATAAATTTAT
Found at i:60370 original size:13 final size:13
Alignment explanation
Indices: 60347--60401 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
60337 AATGACGCGC
*
60347 AATGAGCGTCATA
1 AATGCGCGTCATA
*
60360 AATGCGTGTCATA
1 AATGCGCGTCATA
*
60373 AATGAGCGTCATA
1 AATGCGCGTCATA
60386 AATGCGCGTCATA
1 AATGCGCGTCATA
60399 AAT
1 AAT
60402 TTATGATGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:60376 original size:26 final size:26
Alignment explanation
Indices: 60347--60401 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
60337 AATGACGCGC
*
60347 AATGAGCGTCATAAATGCGTGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
60373 AATGAGCGTCATAAATGCGCGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
60399 AAT
1 AAT
60402 TTATGATGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGCGTCATA
Found at i:64581 original size:21 final size:21
Alignment explanation
Indices: 64557--64598 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
64547 TTCTGGGAAG
* *
64557 GTGTATCGATGCACTATGAAT
1 GTGTACCGATGCACTAAGAAT
64578 GTGTACCGATGCACTAAGAAT
1 GTGTACCGATGCACTAAGAAT
64599 AATTTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (21 bp):
GTGTACCGATGCACTAAGAAT
Found at i:65580 original size:23 final size:23
Alignment explanation
Indices: 65545--65612 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
65535 AATCTTATAT
*
65545 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
65568 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
65591 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
65613 AGCTGTGATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:70755 original size:23 final size:23
Alignment explanation
Indices: 70729--70786 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
70719 ATCTTATATG
70729 GCACTTCGGTGCAATTCTACACT-
1 GCACTTCGGTGCAATTCTAC-CTA
* * *
70752 GCACTACAGTGCAATTCTACGTA
1 GCACTTCGGTGCAATTCTACCTA
70775 GCACTTCGGTGC
1 GCACTTCGGTGC
70787 TTTTATACGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACCTA
Found at i:75901 original size:29 final size:29
Alignment explanation
Indices: 75886--75949 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
75876 ATCTCATGTC
75886 GAATCAGGAAGAGAATCAAATCCCATGCA
1 GAATCAGGAAGAGAATCAAATCCCATGCA
* *
75915 GAATCAGGACGAGAATCAAATACCATGCA
1 GAATCAGGAAGAGAATCAAATCCCATGCA
75944 GAATCA
1 GAATCA
75950 AGATTGCATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (29 bp):
GAATCAGGAAGAGAATCAAATCCCATGCA
Found at i:76983 original size:25 final size:25
Alignment explanation
Indices: 76946--77039 Score: 82
Period size: 25 Copynumber: 3.6 Consensus size: 25
76936 TTTTAATTTT
*
76946 AATATTAA-CTTTTTAAATAAATTA
1 AATATTAATATTTTTAAATAAATTA
*
76970 AATATTAATATTTTTGATATTATATTATATA
1 AATATTAATATTTTT-A-A--ATA-AAT-TA
* *
77001 TATATTAATTTTTTTAAATAAATTA
1 AATATTAATATTTTTAAATAAATTA
*
77026 AATATTAAAATTTT
1 AATATTAATATTTT
77040 AATATTATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
24 8 0.15
25 18 0.33
26 3 0.05
27 4 0.07
29 4 0.07
30 3 0.05
31 15 0.27
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (25 bp):
AATATTAATATTTTTAAATAAATTA
Found at i:77022 original size:56 final size:55
Alignment explanation
Indices: 76947--77066 Score: 181
Period size: 55 Copynumber: 2.2 Consensus size: 55
76937 TTTAATTTTA
* * * *
76947 ATATTAA-CTTTTTAAATAAATTAAATATTAATATTTTTGATATTATATTATATAT
1 ATATTAATTTTTTTAAATAAATTAAATATTAA-AATTTTAATATTATATTATAGAT
77002 ATATTAATTTTTTTAAATAAATTAAATATTAAAATTTTAATATTATATTATAGAT
1 ATATTAATTTTTTTAAATAAATTAAATATTAAAATTTTAATATTATATTATAGAT
77057 AT-TTAATTTT
1 ATATTAATTTT
77067 ATATCATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
54 8 0.13
55 29 0.48
56 23 0.38
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (55 bp):
ATATTAATTTTTTTAAATAAATTAAATATTAAAATTTTAATATTATATTATAGAT
Found at i:77038 original size:27 final size:27
Alignment explanation
Indices: 76955--77039 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
76945 TAATATTAAC
*
76955 TTTTTAAATAAATTAAATATTAATA-T
1 TTTTTAAATAAATTAAATATTAAAATT
* * * * *
76981 TTTTGATATTATATTATATATATATTAATT
1 TTTTTA-AATAAATTAAATAT-TA-AAATT
77011 TTTTTAAATAAATTAAATATTAAAATT
1 TTTTTAAATAAATTAAATATTAAAATT
77038 TT
1 TT
77040 AATATTATAT
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
26 5 0.11
27 17 0.39
28 4 0.09
29 12 0.27
30 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
TTTTTAAATAAATTAAATATTAAAATT
Found at i:77078 original size:56 final size:56
Alignment explanation
Indices: 76947--77081 Score: 177
Period size: 55 Copynumber: 2.4 Consensus size: 56
76937 TTTAATTTTA
* * * *
76947 ATATTAACTTTTT-AAATAAATTAAATATTAATATTTTTGATATTATATTATATAT
1 ATATTAATTTTTTCAAATAAATTAAATATTAATAATTTTAATATTATATTATAGAT
*
77002 ATATTAATTTTTTTAAATAAATTAAATATTAA-AATTTTAATATTATATTATAGAT
1 ATATTAATTTTTTCAAATAAATTAAATATTAATAATTTTAATATTATATTATAGAT
*
77057 AT-TTAATTTTATATCATATAAATTA
1 ATATTAATTTT-T-TCAAATAAATTA
77082 TTTTATATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
54 8 0.11
55 35 0.49
56 28 0.39
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (56 bp):
ATATTAATTTTTTCAAATAAATTAAATATTAATAATTTTAATATTATATTATAGAT
Found at i:77122 original size:20 final size:19
Alignment explanation
Indices: 77062--77123 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
77052 TAGATATTTA
*
77062 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
77081 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
77099 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
77119 ATTTT
1 ATTTT
77124 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:79334 original size:45 final size:46
Alignment explanation
Indices: 79284--79436 Score: 179
Period size: 45 Copynumber: 3.4 Consensus size: 46
79274 GCACCAATCC
* * *
79284 ATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATACATTTT
1 ATGCATCGATGCACTC-TGGATTATATTGAAACATCGAATGCATTTT
* * *
79329 ATGCATCGATGCACTCTAGATTTTA-TGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCTGGATTATATTG-AAACATCGAATGCATTTT
* *
79375 ATCCATCGATGCACTCTGG-TTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCTGGATTATATTGAAACATCGAATGCATTTT
*
79420 ATGCATCGTTGCACTCT
1 ATGCATCGATGCACTCT
79437 TAGTGCACCG
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
44 2 0.02
45 54 0.59
46 35 0.38
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (46 bp):
ATGCATCGATGCACTCTGGATTATATTGAAACATCGAATGCATTTT
Found at i:85180 original size:21 final size:22
Alignment explanation
Indices: 85151--85209 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
85141 TGCATCCCTT
85151 TGAATGTGCATCGATACA-CCA
1 TGAATGTGCATCGATACAGCCA
* * * *
85172 TGAAGGTGCACCGATGCATGCCT
1 TGAATGTGCATCGATACA-GCCA
85195 TGAATGTGCATCGAT
1 TGAATGTGCATCGAT
85210 GCACACTGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.50
23 15 0.50
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (22 bp):
TGAATGTGCATCGATACAGCCA
Found at i:85203 original size:23 final size:22
Alignment explanation
Indices: 85132--85212 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
85122 ACACTTAACA
85132 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
* * *
85156 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
85177 GTGCACCGATGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
85200 GTGCATCGATGCA
1 GTGCATCGATGCA
85213 CACTGTCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 18 0.38
24 12 0.26
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:87513 original size:21 final size:22
Alignment explanation
Indices: 87462--87513 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
87452 ATTTAACAAA
87462 AAGGGGGAGAAATGTTAAATGT
1 AAGGGGGAGAAATGTTAAATGT
* * *
87484 TATGGGGAGAAGTGTTAAA-GT
1 AAGGGGGAGAAATGTTAAATGT
87505 AAGGGGGAG
1 AAGGGGGAG
87514 TAATTTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.37, C:0.00, G:0.42, T:0.21
Consensus pattern (22 bp):
AAGGGGGAGAAATGTTAAATGT
Found at i:87927 original size:46 final size:46
Alignment explanation
Indices: 87868--87977 Score: 152
Period size: 46 Copynumber: 2.4 Consensus size: 46
87858 TGCACCAATC
*
87868 CATGCATCGATGCACTC-AG-GATTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCTAGCGATTTT-TG-AAACATCAAATGCATTT
* * *
87914 GATGCATCGATGCAATCTAGCTATTTTTGAAACATCAAATGCATTT
1 CATGCATCGATGCACTCTAGCGATTTTTGAAACATCAAATGCATTT
87960 CATGCATCGATGCACTCT
1 CATGCATCGATGCACTCT
87978 TAGTGTACCG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 47 0.84
47 4 0.07
48 5 0.09
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (46 bp):
CATGCATCGATGCACTCTAGCGATTTTTGAAACATCAAATGCATTT
Found at i:89884 original size:130 final size:131
Alignment explanation
Indices: 89600--89918 Score: 345
Period size: 130 Copynumber: 2.4 Consensus size: 131
89590 GAGTGACGCA
* * * * *
89600 GCTCCTACGTGATGAGGAGATCTAGTTGAGGGATGACACGGCTCATATGTGATGAAGAGTTCTGG
1 GCTCCTACGTGATGAGGAGGTCTGGTAG-GGGATGACACGGCTCATACGTGATGAAAAGTTCTGG
* * *** * *
89665 CCATCTTTAGGTATGGTGATAACATGGTTCTTAGGCGATGAGGACGACTGGTTATCTAGGGGTGA
65 CCATATTTAGG--TGATGATAACACAATTCTTAGACGACGAGGACGACTGGTTATCTAGGGGTGA
89730 CACG
128 CACG
*
89734 GCTCCTACGTGATGAGGAGGTCTGGTCGGGGATGACACGGCTCATACGTGATGAAAAG-TCATGG
1 GCTCCTACGTGATGAGGAGGTCTGGTAGGGGATGACACGGCTCATACGTGATGAAAAGTTC-TGG
* * * * * ** *
89798 CCATATTTAGG-GATGATAACACAATTTTTATATGACGATGACGGCTGGTTATCTTTGGTTGACA
65 CCATATTTAGGTGATGATAACACAATTCTTAGACGACGAGGACGACTGGTTATCTAGGGGTGACA
89862 CG
130 CG
* ** * *
89864 GCTTCTACGTGATGAGGAGGTCTGGTTAGGGGATGGTATGGTTCATACGTGATGA
1 GCTCCTACGTGATGAGGAGGTCTGG-TAGGGGATGACACGGCTCATACGTGATGA
89919 GGATGGCAAG
Statistics
Matches: 157, Mismatches: 26, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
130 65 0.41
131 24 0.15
132 2 0.01
133 41 0.26
134 25 0.16
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (131 bp):
GCTCCTACGTGATGAGGAGGTCTGGTAGGGGATGACACGGCTCATACGTGATGAAAAGTTCTGGC
CATATTTAGGTGATGATAACACAATTCTTAGACGACGAGGACGACTGGTTATCTAGGGGTGACAC
G
Found at i:89987 original size:28 final size:28
Alignment explanation
Indices: 89955--90009 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
89945 TGGTTTTAGG
* *
89955 AGAAACTGACTAAAAGGTTTGTTTCAAA
1 AGAAACAGACTAAAAGATTTGTTTCAAA
*
89983 AGAAACAGACTCAAAGATTTGTTTCAA
1 AGAAACAGACTAAAAGATTTGTTTCAA
90010 TAAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (28 bp):
AGAAACAGACTAAAAGATTTGTTTCAAA
Found at i:90040 original size:31 final size:28
Alignment explanation
Indices: 89967--90043 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 28
89957 AAACTGACTA
* * *
89967 AAAGGTTTGTTTCAAAAGAAACAGACTC
1 AAAGATTTGTTTCAAAAGAAAAAAACTC
89995 AAAGATTTGTTTCAATAA-AAAAAAACTC
1 AAAGATTTGTTTCAA-AAGAAAAAAACTC
90023 AAAGATAGTGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
90044 CAACTGTCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 28 0.68
29 2 0.05
30 3 0.07
31 8 0.20
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAAAAAACTC
Found at i:90826 original size:36 final size:34
Alignment explanation
Indices: 90785--90885 Score: 114
Period size: 36 Copynumber: 2.9 Consensus size: 34
90775 TTGTATCTCA
*
90785 GAGAAAAAATGTCTCAAGCGAGACAAAATTTATTTT
1 GAGAAAAAATGTCTCAAGCGAGACAAAA-TT-TTCT
* *
90821 GAGAAAAATTGTCTCAAACGAGACAAAATTTTCT
1 GAGAAAAAATGTCTCAAGCGAGACAAAATTTTCT
* * * *
90855 -AGAAAAAATATCTAAAGCGAGATAGAATTTT
1 GAGAAAAAATGTCTCAAGCGAGACAAAATTTT
90886 GTTTCAAGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
33 25 0.45
34 3 0.05
35 2 0.04
36 26 0.46
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (34 bp):
GAGAAAAAATGTCTCAAGCGAGACAAAATTTTCT
Found at i:90876 original size:33 final size:34
Alignment explanation
Indices: 90785--90885 Score: 107
Period size: 33 Copynumber: 2.9 Consensus size: 34
90775 TTGTATCTCA
* *
90785 GAGAAAAAATGTCTCAAGCGAGACAAAATTTATTTT
1 GAGAAAAAATGTCTAAAGCGAGACAAAA-TT-TTCT
*
90821 GAGAAAAATTGTCTCAAA-CGAGACAAAATTTTCT
1 GAGAAAAAATGTCT-AAAGCGAGACAAAATTTTCT
* * *
90855 -AGAAAAAATATCTAAAGCGAGATAGAATTTT
1 GAGAAAAAATGTCTAAAGCGAGACAAAATTTT
90886 GTTTCAAGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
32 3 0.05
33 23 0.41
34 3 0.05
35 2 0.04
36 23 0.41
37 2 0.04
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (34 bp):
GAGAAAAAATGTCTAAAGCGAGACAAAATTTTCT
Found at i:91224 original size:14 final size:15
Alignment explanation
Indices: 91198--91230 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
91188 TGCAAATTTC
91198 ATGTGTCATGTATGT
1 ATGTGTCATGTATGT
91213 ATGTGT-ATGTATGT
1 ATGTGTCATGTATGT
91227 ATGT
1 ATGT
91231 TGATATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.21, C:0.03, G:0.27, T:0.48
Consensus pattern (15 bp):
ATGTGTCATGTATGT
Found at i:94956 original size:31 final size:30
Alignment explanation
Indices: 94918--94977 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
94908 AAAATGATAT
94918 AAACAAAAGAAAAGAAATAAGTTATATACAC
1 AAACAAAAGAAAAGAAATAAGTTA-ATACAC
* *
94949 AAACAAAAGAAAATAAATTAGTTAATACA
1 AAACAAAAGAAAAGAAATAAGTTAATACA
94978 GGTAAGACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.18
Consensus pattern (30 bp):
AAACAAAAGAAAAGAAATAAGTTAATACAC
Found at i:96047 original size:17 final size:17
Alignment explanation
Indices: 96025--96058 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
96015 TAAAACGTCT
96025 TTTAAAACAATTTTAAG
1 TTTAAAACAATTTTAAG
96042 TTTAAAACAATTTTAAG
1 TTTAAAACAATTTTAAG
96059 GAAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
TTTAAAACAATTTTAAG
Found at i:98293 original size:3 final size:3
Alignment explanation
Indices: 98285--98311 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
98275 TTAATAAACC
98285 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
98312 ATTAATTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:99404 original size:14 final size:14
Alignment explanation
Indices: 99385--99411 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
99375 TCGGATGTTT
99385 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
99399 TCGGATGGCCTCG
1 TCGGATGGCCTCG
99412 AATGCCCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.41, T:0.22
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:102087 original size:37 final size:36
Alignment explanation
Indices: 102031--102147 Score: 175
Period size: 35 Copynumber: 3.2 Consensus size: 36
102021 CCCATTATCA
* * *
102031 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCAT
102067 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
102102 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCATT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-T
102139 TTTTCAAAG
1 TTTTCAAAG
102148 TTGGTTACCA
Statistics
Matches: 75, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
35 35 0.47
36 11 0.15
37 29 0.39
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
Found at i:102103 original size:21 final size:21
Alignment explanation
Indices: 102079--102139 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
102069 TTCAAAGAAA
102079 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
102100 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
102114 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
102135 CATTT
1 CATTT
102140 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:102156 original size:35 final size:36
Alignment explanation
Indices: 102046--102174 Score: 142
Period size: 35 Copynumber: 3.6 Consensus size: 36
102036 AACAAACATC
* *
102046 TACCAAACTTTGAAAAAC-TATTTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCAT-TTTTTCAAAG-AACAGT
*
102083 TACCAAACTTTGAAAACCA--TTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAG-AACAGT
***
102118 TACCAAACTTTGAAAACCATTTTTTCAAAG-TTGGT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
102153 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACCATTTT
102175 AATACTTTCA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
34 14 0.17
35 44 0.52
37 26 0.31
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (36 bp):
TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
Found at i:106235 original size:16 final size:16
Alignment explanation
Indices: 106211--106243 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
106201 TATCGCCGAC
*
106211 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
106227 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
106243 C
1 C
106244 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:106700 original size:37 final size:36
Alignment explanation
Indices: 106642--106760 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
106632 TCCCATTATC
* *
106642 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
106678 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
*
106714 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
106749 ATTTTTTCAAAG
1 A-TTTTTCAAAG
106761 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 34 0.44
36 14 0.18
37 29 0.38
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
Found at i:112330 original size:5 final size:5
Alignment explanation
Indices: 112320--112353 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
112310 TGGTCATTTC
112320 TTTTA TTTTA TGTTTA TTTTA TTTTA TGTTTA TT
1 TTTTA TTTTA T-TTTA TTTTA TTTTA T-TTTA TT
112354 AGTGTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 17 0.63
6 10 0.37
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:112337 original size:11 final size:10
Alignment explanation
Indices: 112320--112353 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
112310 TGGTCATTTC
112320 TTTTATTTTA
1 TTTTATTTTA
112330 TGTTTATTTTA
1 T-TTTATTTTA
112341 TTTTATGTTTA
1 TTTTAT-TTTA
112352 TT
1 TT
112354 AGTGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:112341 original size:16 final size:16
Alignment explanation
Indices: 112320--112353 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
112310 TGGTCATTTC
112320 TTTTATTTTATGTTTA
1 TTTTATTTTATGTTTA
112336 TTTTATTTTATGTTTA
1 TTTTATTTTATGTTTA
112352 TT
1 TT
112354 AGTGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTTTATGTTTA
Found at i:122406 original size:22 final size:22
Alignment explanation
Indices: 122381--122432 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
122371 CAATTCATTT
* *
122381 TCTTCTCTTTTTTATCTTATTC
1 TCTTCTCTTCTTTATATTATTC
* *
122403 TCTTCTATTCTTTATATTCTTC
1 TCTTCTCTTCTTTATATTATTC
122425 TCTTCTCT
1 TCTTCTCT
122433 AACGTGAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (22 bp):
TCTTCTCTTCTTTATATTATTC
Found at i:122986 original size:20 final size:20
Alignment explanation
Indices: 122961--123005 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
122951 GTAAGGGTAC
122961 CGATACCTCAAGGGATGTAT
1 CGATACCTCAAGGGATGTAT
*
122981 CGATACCTCAAGGGGTGTAT
1 CGATACCTCAAGGGATGTAT
123001 CGATA
1 CGATA
123006 ACCCCTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
CGATACCTCAAGGGATGTAT
Found at i:123414 original size:10 final size:12
Alignment explanation
Indices: 123388--123415 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
123378 TGTCTACGCG
123388 ATATAAGAAGTT
1 ATATAAGAAGTT
123400 ATATAAGAAGTT
1 ATATAAGAAGTT
123412 ATAT
1 ATAT
123416 GTCTACGCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (12 bp):
ATATAAGAAGTT
Found at i:130772 original size:40 final size:40
Alignment explanation
Indices: 130717--130798 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
130707 AGTTCTCTAT
*
130717 TTGAAATTATTAATTACTCATTTTGATCGTATATAAAGGC
1 TTGAAATTATTAATTACTCATTTTGATCATATATAAAGGC
*
130757 TTGAAATTATTAATTACTCATTTTGATTATATATAAAGGC
1 TTGAAATTATTAATTACTCATTTTGATCATATATAAAGGC
130797 TT
1 TT
130799 AATTAAGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (40 bp):
TTGAAATTATTAATTACTCATTTTGATCATATATAAAGGC
Found at i:131043 original size:12 final size:12
Alignment explanation
Indices: 131010--131052 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
131000 TGTTATTATT
*
131010 TTATTAATAAAA
1 TTATTAAAAAAA
*
131022 TTGATAAAAAAAA
1 TT-ATTAAAAAAA
*
131035 TTATTAAAAATA
1 TTATTAAAAAAA
131047 TTATTA
1 TTATTA
131053 TTTTTATCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
TTATTAAAAAAA
Found at i:131200 original size:21 final size:21
Alignment explanation
Indices: 131176--131219 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
131166 TCTGAAATGT
131176 TAAAAA-AATTAATATTTTAAA
1 TAAAAATAA-TAATATTTTAAA
*
131197 TAAAAATAATAATTTTTTAAA
1 TAAAAATAATAATATTTTAAA
131218 TA
1 TA
131220 TTTTTTTACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:131206 original size:18 final size:18
Alignment explanation
Indices: 131175--131212 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
131165 ATCTGAAATG
*
131175 TTAAAAAAATTAAT-ATT
1 TTAAAAAAAATAATAATT
131192 TTAAATAAAAATAATAATT
1 TTAAA-AAAAATAATAATT
131211 TT
1 TT
131213 TTAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAAAAAAATAATAATT
Found at i:131968 original size:17 final size:18
Alignment explanation
Indices: 131946--131979 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
131936 AAACTTTAAC
*
131946 AAAATATTTA-TAAATAG
1 AAAATATGTAGTAAATAG
131963 AAAATATGTAGTAAATA
1 AAAATATGTAGTAAATA
131980 TTTGAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (18 bp):
AAAATATGTAGTAAATAG
Found at i:132523 original size:21 final size:20
Alignment explanation
Indices: 132490--132528 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
132480 ATGGGAACTT
* *
132490 AAAAATTTGAGTCGACTCGA
1 AAAAATTTAAGTCAACTCGA
132510 AAAAATTTCAAGTCAACTC
1 AAAAATTT-AAGTCAACTC
132529 CGAGTTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (20 bp):
AAAAATTTAAGTCAACTCGA
Found at i:133703 original size:7 final size:7
Alignment explanation
Indices: 133691--133722 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
133681 GGTTTGCATC
133691 GGAGAGT
1 GGAGAGT
133698 GGAGAGT
1 GGAGAGT
133705 GGAGAGT
1 GGAGAGT
133712 GGAGAGT
1 GGAGAGT
133719 GGAG
1 GGAG
133723 GACGAAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.59, T:0.12
Consensus pattern (7 bp):
GGAGAGT
Found at i:147486 original size:23 final size:23
Alignment explanation
Indices: 147460--147537 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
147450 CACCACAGCT
147460 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
147483 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
147506 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
147529 TATAATAAT
1 CAT-ATAAT
147538 GTCCATAAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:147728 original size:104 final size:103
Alignment explanation
Indices: 147548--147762 Score: 367
Period size: 104 Copynumber: 2.1 Consensus size: 103
147538 GTCCATAAGT
* ** *
147548 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCAAACT
147613 TCACACATGTTCCAAAGAATACATATATGTCCCAAAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCC-AAAGG
*
147652 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCAAACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCAAACT
*
147717 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCAAAGG
147755 ACCACATA
1 ACCACATA
147763 GACCCTCGAC
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
103 12 0.11
104 93 0.89
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCAAACT
TCACACATGTTCCAAAGAATACATATATGTCCCAAAGG
Found at i:160670 original size:23 final size:23
Alignment explanation
Indices: 160644--160704 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
160634 GTCACCAACT
160644 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
160667 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
160690 CGTAGAATTGCACCG
1 CATATAATTGCACCG
160705 TAGTACCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:160906 original size:103 final size:103
Alignment explanation
Indices: 160727--160944 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
160717 TAATGCCCAT
* * *
160727 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATGTGTCTCACCA
160792 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
160830 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAATATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATGTGTCTCACCA
*
160895 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
160933 AATGACCACATA
1 AAGGACCACATA
160945 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Done.